Just Cause 2!
I should probably stop blurting that out, but it's so much fun from a mindless actioney perspective. The game can be completed doing like only one faction mission, but I'd say they're pretty integral to gamplay (or are at least supposed to be.)
I personally didn't like any of the S.T.A.L.K.E.R. games, but I was mildly impressed by FarCry2 and it's factions. Actually, I'm probably just not that into factions in games.